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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data_10 when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.13

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-10-24, 20:36 CST based on data in: /home/qinchunyuan/proteomicsDIA/mzml/diatest


        pmultiqc

        pmultiqc is a multiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms.

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.

        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 6/6 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        QPLAP418AT_MS1_oecf1-SK0563-49.mzML5115
        Liver_NASH
        5
        QPLAP426AK_MS1_oecf1-SK0563-04.mzML4114
        Liver_NASH
        4
        QPLAP454AP_MS1_oecf1-SK0563-156.mzML3113
        Healthy
        3
        QPLAP460A0_MS1_oecf1-SK0563-18.mzML6116
        Liver_NASH
        6
        QPLAP469A4_MS1_oecf1-SK0563-21.mzML1111
        Healthy
        1
        QPLAP470A7_MS1_oecf1-SK0563-46.mzML2112
        Healthy
        2

        Summary Table

        This table shows the quantms pipeline summary statistics

        This table shows the quantms pipeline summary statistics

        Showing 1/1 rows and 2/2 columns.
        #MS2 Spectra#Peptides Quantified#Proteins Quantified
        564468
        52112
        4702

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 6/6 rows and 7/7 columns.
        Spectra FileSample NameConditionFraction#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
        QPLAP418AT_MS1_oecf1-SK0563-49.mzML5
        Liver_NASH
        1
        46206
        46206
        14453
        5315
        QPLAP426AK_MS1_oecf1-SK0563-04.mzML4
        Liver_NASH
        1
        42149
        42149
        13485
        5157
        QPLAP454AP_MS1_oecf1-SK0563-156.mzML3
        Healthy
        1
        44985
        44985
        14642
        5156
        QPLAP460A0_MS1_oecf1-SK0563-18.mzML6
        Liver_NASH
        1
        44582
        44581
        14291
        5212
        QPLAP469A4_MS1_oecf1-SK0563-21.mzML1
        Healthy
        1
        43367
        43366
        13850
        5151
        QPLAP470A7_MS1_oecf1-SK0563-46.mzML2
        Healthy
        1
        44720
        44720
        13990
        5200

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (mainly the mzTab file).

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Click Show replicates to switch to bar plots for every replicate.
        Showing 50/50 rows and 9/9 columns.
        PeptideIDPeptideSequenceModificationProteinNameBestSearchScoreAverage IntensityHealthyLiver_NASHHealthyLiver_NASH
        1
        AAAAAAAAAAAAAAAASAGGKEAASGPNDS
        nan
        SP9_HUMAN
        0.99997
        5.532
        5.53896
        5.51692
        2
        AAAACLDK
        5-Carbamidomethyl
        UN45A_HUMAN
        0.99978
        5.264
        4.83435
        5.47554
        3
        AAAATGTIFTFR
        nan
        IPSP_HUMAN
        1.00000
        6.453
        6.39192
        6.50660
        4
        AAADFATHGK
        nan
        MICA1_HUMAN
        1.00000
        5.281
        5.32443
        5.23332
        5
        AAADTLQGPMQAAYR
        nan
        EDC4_HUMAN
        0.99997
        5.970
        5.93806
        6.01292
        6
        AAAEAAVPR
        nan
        SPN90_HUMAN
        1.00000
        6.102
        6.02680
        6.16598
        7
        AAAEDVNVTFEDQQK
        nan
        PFD4_HUMAN
        0.99962
        5.774
        0.00000
        5.77409
        8
        AAAEELLAR
        nan
        SHIP2_HUMAN
        0.99979
        6.092
        6.10181
        6.07743
        9
        AAAELALSCLPHAHALNPNEIQR
        9-Carbamidomethyl
        ZSWM8_HUMAN
        0.99997
        5.914
        5.87518
        5.95043
        10
        AAAEVNQDYGLDPK
        nan
        FUMH_HUMAN
        1.00000
        6.621
        6.57327
        6.66429
        11
        AAAFEEQENETVVVK
        nan
        TLN1_HUMAN
        0.99999
        7.912
        7.85005
        7.96679
        12
        AAAFEEQENETVVVKEK
        nan
        TLN1_HUMAN
        1.00000
        7.338
        7.46783
        7.15179
        13
        AAAFEQLQK
        nan
        TOM70_HUMAN
        0.99998
        6.010
        6.01036
        0.00000
        14
        AAAGAAGAEAPR
        nan
        EX3L4_HUMAN
        1.00000
        5.491
        5.50044
        5.48038
        15
        AAAGGLAMLTSMRPTLCSR
        17-Carbamidomethyl
        UN45A_HUMAN
        1.00000
        6.392
        6.41808
        6.36484
        16
        AAAGGLAMLTSMRPTLCSR
        8-Oxidation,12-Oxidation,17-Carbamidomethyl
        UN45A_HUMAN
        0.99997
        5.839
        5.84605
        5.83239
        17
        AAAGGLAMLTSMRPTLCSR
        8-Oxidation,17-Carbamidomethyl
        UN45A_HUMAN
        1.00000
        5.943
        6.05627
        5.78995
        18
        AAAGLGGGDSGDGTAR
        nan
        RUFY1_HUMAN
        1.00000
        5.927
        5.96453
        5.88506
        19
        AAAGSLPGLQAQLAQAEQR
        nan
        FYCO1_HUMAN
        0.99992
        5.658
        5.72323
        5.53621
        20
        AAAHCAHVFTTVSQITAIEAQHLLK
        5-Carbamidomethyl
        GYS1_HUMAN
        1.00000
        5.914
        5.88911
        5.94321
        21
        AAAIGIDLGTTYSCVGVFQHGK
        14-Carbamidomethyl
        HS71A_HUMAN;HS71B_HUMAN
        1.00000
        7.226
        7.16038
        7.28310
        22
        AAALASLKK
        nan
        SPTC1_HUMAN
        0.99998
        5.427
        5.34580
        5.47341
        23
        AAALATVNAWAEQTGMKEWLEGEDLSEELKK
        nan
        CKAP5_HUMAN
        1.00000
        6.239
        6.16963
        6.32552
        24
        AAALCNACELSGK
        5-Carbamidomethyl,8-Carbamidomethyl
        TPC11_HUMAN
        1.00000
        6.159
        6.17764
        6.13990
        25
        AAALDPAWPEPR
        nan
        TTC5_HUMAN
        0.99996
        6.338
        6.33886
        6.33712
        26
        AAALEAMKDYTK
        nan
        STIP1_HUMAN
        1.00000
        6.342
        6.38865
        6.26252
        27
        AAALEFLNR
        nan
        STIP1_HUMAN
        0.99996
        6.662
        6.55293
        6.74831
        28
        AAALEFLNRFEEAK
        nan
        STIP1_HUMAN
        0.99999
        5.859
        5.83153
        5.88487
        29
        AAALEFLNRFEEAKR
        nan
        STIP1_HUMAN
        1.00000
        6.300
        6.39093
        6.18476
        30
        AAALEQFK
        nan
        NNTM_HUMAN
        0.99999
        6.843
        6.77856
        6.89957
        31
        AAALLLQNDNNADVESK
        nan
        ANK3_HUMAN
        0.99984
        5.674
        0.00000
        5.67402
        32
        AAALSFVSLVDGYFR
        nan
        TYK2_HUMAN
        0.99999
        5.658
        5.70310
        5.61882
        33
        AAALSLSTLASPK
        nan
        EFNB1_HUMAN
        1.00000
        6.701
        6.67934
        6.72144
        34
        AAALVLQTIWGYK
        nan
        CTND1_HUMAN
        0.99996
        6.210
        6.33368
        6.03637
        35
        AAAMTPPEEELKR
        4-Oxidation
        RB3GP_HUMAN
        0.99997
        5.854
        5.82280
        5.88309
        36
        AAAMTPPEEELKR
        nan
        RB3GP_HUMAN
        0.99997
        5.990
        5.94697
        6.03736
        37
        AAANEQLTR
        nan
        MIC19_HUMAN
        1.00000
        5.320
        5.24334
        5.38543
        38
        AAAPAPEEEMDECEQALAAEPK
        10-Oxidation,13-Carbamidomethyl
        EF1G_HUMAN
        0.99997
        5.505
        5.46054
        5.54531
        39
        AAAPAPEEEMDECEQALAAEPK
        13-Carbamidomethyl
        EF1G_HUMAN
        0.99987
        5.842
        5.78589
        5.89149
        40
        AAAPAPVSEAVCR
        12-Carbamidomethyl
        ICAL_HUMAN
        0.99996
        6.042
        0.00000
        6.04174
        41
        AAAPCIIFFDELDSLAPSR
        5-Carbamidomethyl
        PEX6_HUMAN
        0.99997
        5.058
        5.16297
        4.91806
        42
        AAAPGTAVLLVTANVGSLFDDPENLQK
        nan
        I5P1_HUMAN
        1.00000
        5.856
        5.90631
        5.79836
        43
        AAAPLFTGFLVLHSEPR
        nan
        MROH1_HUMAN
        0.99999
        5.784
        5.80170
        5.76569
        44
        AAAQCYIDLIIK
        5-Carbamidomethyl
        COPB_HUMAN
        1.00000
        6.303
        6.28038
        6.32118
        45
        AAAQCYIDLIIKESDNNVK
        5-Carbamidomethyl
        COPB_HUMAN
        0.99998
        5.949
        6.11944
        5.66467
        46
        AAAQLLQSQAQQSGAQQTK
        nan
        SEP11_HUMAN
        1.00000
        6.147
        6.08862
        6.19792
        47
        AAAQLLQSQAQQSGAQQTKK
        nan
        SEP11_HUMAN
        1.00000
        5.507
        5.56322
        5.44337
        48
        AAAQLTYCSLCPPDDLADR
        8-Carbamidomethyl,11-Carbamidomethyl
        LOX12_HUMAN
        1.00000
        7.290
        7.31790
        7.25934
        49
        AAAQLTYCSLCPPDDLADRGLLGLPGALYAHDALR
        8-Carbamidomethyl,11-Carbamidomethyl
        LOX12_HUMAN
        0.99997
        5.968
        6.12215
        5.52814
        50
        AAASGNENIQPPPLAYK
        nan
        RBGPR_HUMAN
        0.99973
        5.834
        5.84684
        5.81359
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (mainly the mzTab file).

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.

        Click Show replicates to switch to bar plots of quantities in each replicate.

        Showing 50/50 rows and 7/7 columns.
        ProteinIDProteinNamePeptides_NumberAverage IntensityHealthyLiver_NASHHealthyLiver_NASH
        1
        (Bos
        8
        7.375
        6.32923
        7.38243
        2
        1433B_HUMAN
        8
        7.174
        7.06849
        7.25688
        3
        1433E_HUMAN
        22
        8.206
        8.14493
        8.25574
        4
        1433F_HUMAN
        19
        7.940
        7.91030
        7.96128
        5
        1433G_HUMAN
        14
        7.647
        7.60052
        7.68145
        6
        1433S_HUMAN
        1
        7.488
        7.41526
        7.54996
        7
        1433T_HUMAN
        16
        7.403
        7.31431
        7.45206
        8
        1433Z_HUMAN
        30
        9.098
        9.07224
        9.12158
        9
        2A5A_HUMAN
        16
        7.165
        7.07534
        7.17896
        10
        2A5D_HUMAN
        14
        6.981
        6.98120
        6.97717
        11
        2A5E_HUMAN
        9
        6.657
        6.64166
        6.67257
        12
        2A5G_HUMAN
        3
        6.138
        6.14897
        6.09778
        13
        2AAA_HUMAN
        36
        8.065
        8.02093
        8.09977
        14
        2ABA_HUMAN
        12
        7.165
        7.15324
        7.18483
        15
        2ABD_HUMAN
        3
        6.238
        6.28875
        6.17939
        16
        3BP1_HUMAN
        3
        5.896
        5.63083
        5.97216
        17
        3BP5L_HUMAN
        1
        5.072
        0.00000
        5.07162
        18
        3BP5_HUMAN
        1
        5.565
        5.48850
        5.62979
        19
        3HIDH_HUMAN
        4
        6.389
        6.36245
        6.41394
        20
        4F2_HUMAN
        11
        7.064
        6.98807
        7.12576
        21
        5HT2A_HUMAN
        1
        5.463
        5.46268
        0.00000
        22
        5NT3A_HUMAN
        18
        7.182
        7.12478
        7.19647
        23
        5NTC_HUMAN
        15
        7.243
        7.25636
        7.23218
        24
        6PGD_HUMAN
        30
        8.333
        8.29914
        8.36043
        25
        6PGL_HUMAN
        12
        7.681
        7.66164
        7.69882
        26
        A16A1_HUMAN
        27
        7.831
        7.85576
        7.80292
        27
        A16L1_HUMAN
        1
        5.952
        5.89417
        6.00344
        28
        A1AG1_HUMAN
        11
        7.710
        7.39537
        7.86188
        29
        A1AG2_HUMAN
        6
        7.168
        6.95979
        7.30362
        30
        A1AT_HUMAN
        36
        8.931
        8.77824
        9.04078
        31
        A1BG_HUMAN
        19
        8.227
        8.16772
        8.27682
        32
        A2AP_HUMAN
        16
        7.679
        7.68141
        7.68412
        33
        A2GL_HUMAN
        8
        7.207
        7.12594
        7.26956
        34
        A2MG_HUMAN
        96
        9.665
        9.41668
        9.81902
        35
        A4_HUMAN
        30
        8.134
        8.11518
        8.14882
        36
        AAAT_HUMAN
        1
        5.245
        0.00000
        5.24475
        37
        AACS_HUMAN
        2
        5.665
        5.68957
        5.47903
        38
        AACT_HUMAN
        24
        8.263
        8.05597
        8.40088
        39
        AAK1_HUMAN
        1
        5.252
        5.32965
        5.03392
        40
        AAKB1_HUMAN
        2
        5.657
        5.70070
        5.50629
        41
        AAKB2_HUMAN
        2
        5.894
        5.99477
        5.58422
        42
        AAKG1_HUMAN
        17
        7.259
        7.24612
        7.27431
        43
        AAKG2_HUMAN
        3
        5.964
        5.99319
        5.91887
        44
        AAPK1_HUMAN
        19
        7.566
        7.57647
        7.55015
        45
        AASS_HUMAN
        1
        5.223
        5.30529
        5.12092
        46
        AATC_HUMAN
        16
        7.489
        7.52755
        7.44472
        47
        AATM_HUMAN
        24
        7.732
        7.70755
        7.75613
        48
        AB17A_HUMAN;AB17C_HUMAN
        1
        5.257
        5.24630
        5.26841
        49
        AB1IP_HUMAN
        1
        5.268
        5.26818
        0.00000
        50
        ABC3C_HUMAN
        3
        6.061
        5.98662
        6.12461
        First Page Previous PageNext Page Last PagePage/Total Pages